Start off with a medium or fine polishing compound first. If that does not take it out, then move to something more aggressive. If you start with a heavy compound, it will take a lot more work. Usually a rubbing compound like 3M Super Duty may be a bit aggressive. Like I said, start with a polish that is not too aggressive, and work up from there. You will be surprised what you can get out.

Like buzz said if the scratches are not deep in the gelcoat try polish first with a high speed buffer. The buffer heats up the gelcoat and blends it in for a lack of a better description. If you haven't used a high speed buffer before I'd call a buddy that has.

How do you work around stickers/decals/graphics on the boat? I assume a heavy compound would completely destroy them, but what about a fine polishing compound (finishing compound)? I have a good bit of decals on mine.